It has been shown that maternal hyperthyroidism can affects on neonatal outcomes such as spontaneous abortion, intrauterine growth retardation. The aim of this study was to investigate the influence of hyperthyroidism on formation of cerebellar cortical layers in the rat embryos. Thirty Sprague-Dawley female sexually mature rats weighting 200 ± 20 g were used in the study. Female rats were randomly divided into 2 groups. One group as control group did not received any injection. Another group as experimental group (hyperthyroid rats) received L-thyroxine (0.5 mg/kg per day) by IP injection. Serum concentrations of triiodothyronine (T3) and tetraiodothyronine (T4) increased in hyperthyroid rats after two weeks of the start of treatment. All female rats in both groups were mated with normal male rats. Hyperthyroid pregnant rats were received L-thyroxine (0.5 mg/kg per day) by IP injection during the gestation period. Animals were killed on 21th day of gestation and the embryos were taken and their head were cut and fixed in Boin’s solution for 72 hours. Head of embryos were then dehydrated and embedded in paraffin. The paraffin blocks were sagitally sectioned at 5-micrometer thickness and then stained by hematoxylin-eosin method. Quantitative computer-assisted morphometric study was done on the cortical layer of the cerebellum including: External granular layer (EGL), Intermediate layer (IL), and maternal granular layer (IGL). The results showed the thickness of the EGL was decreased in experimental groups when compared to control group (P=0.06). The thickness of the IGL was also was no significant decreased in experimental groups when compared to control group (P=0.09). On the other hand, thickness of IL of experimental group was increased when compared to control group, but the differences were not significant. Our results showed that maternal hyperthyroidism can affects on the formation and neuronal migration in the cerebellar cortex of rat embryos. Therefore, pregnant women with hyperthyroidism should appropriately be managed.